Loading ALL
Results
load("~/GitHub/SurvivalTadpole/RMDS/TADPOLE_BESS_Results.RData")
load("~/GitHub/SurvivalTadpole/RMDS/TADPOLE_LASSO_Results.RData")
load("~/GitHub/SurvivalTadpole/RMDS/TADPOLE_BSWIMS_Results.RData")
par(op)
survmtest <- cvLASSORaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinLASSO <- predictionStats_binary(survmtest[,c(2,3)],"LASSO: MCI to AD Conversion")

survmtest <- cvRIDGERaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinRIDGE <- predictionStats_binary(survmtest[,c(2,3)],"RIDGE: MCI to AD Conversion")

survmtest <- cvBESSRaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBESS <- predictionStats_binary(survmtest[,c(2,3)],"BESS:BIC: MCI to AD Conversion")

survmtest <- cvBESSERaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBESSEBIC <- predictionStats_binary(survmtest[,c(2,3)],"BESS:EBIC: MCI to AD Conversion")

survmtest <- cvBESSGSERaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBESSGS <- predictionStats_binary(survmtest[,c(2,3)],"BESS:GS: MCI to AD Conversion")

survmtest <- cvBSWiMSRaw$survMedianTest
survmtest <- survmtest[complete.cases(survmtest),]
prBinBSWiMS <- predictionStats_binary(survmtest[,c(2,3)],"MCI to AD Conversion")
par(new=TRUE)
plot(prBinLASSO$ROC.analysis$roc.predictor,col="red")
par(new=TRUE)
plot(prBinRIDGE$ROC.analysis$roc.predictor,col="pink")
par(new=TRUE)
plot(prBinBESS$ROC.analysis$roc.predictor,col="blue")
par(new=TRUE)
plot(prBinBESSEBIC$ROC.analysis$roc.predictor,col="cyan")
par(new=TRUE)
plot(prBinBESSGS$ROC.analysis$roc.predictor,col="gold")
legend("bottomright",
legend=c("BSWiMS","LASSO","RIDGE","BIC","EBIC","GS"),
lty=1,
col=c("black","red","pink","blue","cyan","gold"),cex=0.85)

ROC Tests
pander::pander(roc.test(prBinLASSO$ROC.analysis$roc.predictor,prBinBSWiMS$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinLASSO$ROC.analysis$roc.predictor and
prBinBSWiMS$ROC.analysis$roc.predictor
| 0.314 |
0.753 |
two.sided |
0.875 |
0.874 |
pander::pander(roc.test(prBinLASSO$ROC.analysis$roc.predictor,prBinBESSEBIC$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinLASSO$ROC.analysis$roc.predictor and
prBinBESSEBIC$ROC.analysis$roc.predictor
| 3.96 |
7.48e-05 * * * |
two.sided |
0.875 |
0.832 |
pander::pander(roc.test(prBinLASSO$ROC.analysis$roc.predictor,prBinBESSGS$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinLASSO$ROC.analysis$roc.predictor and
prBinBESSGS$ROC.analysis$roc.predictor
| 3.6 |
0.000315 * * * |
two.sided |
0.875 |
0.838 |
pander::pander(roc.test(prBinLASSO$ROC.analysis$roc.predictor,prBinBESS$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinLASSO$ROC.analysis$roc.predictor and
prBinBESS$ROC.analysis$roc.predictor
| 3.96 |
7.48e-05 * * * |
two.sided |
0.875 |
0.832 |
pander::pander(roc.test(prBinLASSO$ROC.analysis$roc.predictor,prBinRIDGE$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinLASSO$ROC.analysis$roc.predictor and
prBinRIDGE$ROC.analysis$roc.predictor
| 9.51 |
1.91e-21 * * * |
two.sided |
0.875 |
0.591 |
pander::pander(roc.test(prBinBSWiMS$ROC.analysis$roc.predictor,prBinBESSEBIC$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinBSWiMS$ROC.analysis$roc.predictor and
prBinBESSEBIC$ROC.analysis$roc.predictor
| 3.95 |
7.97e-05 * * * |
two.sided |
0.874 |
0.832 |
pander::pander(roc.test(prBinBSWiMS$ROC.analysis$roc.predictor,prBinBESSGS$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinBSWiMS$ROC.analysis$roc.predictor and
prBinBESSGS$ROC.analysis$roc.predictor
| 3.59 |
0.000333 * * * |
two.sided |
0.874 |
0.838 |
pander::pander(roc.test(prBinBSWiMS$ROC.analysis$roc.predictor,prBinBESS$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinBSWiMS$ROC.analysis$roc.predictor and
prBinBESS$ROC.analysis$roc.predictor
| 3.95 |
7.97e-05 * * * |
two.sided |
0.874 |
0.832 |
pander::pander(roc.test(prBinBSWiMS$ROC.analysis$roc.predictor,prBinRIDGE$ROC.analysis$roc.predictor))
DeLong’s test for two correlated ROC curves:
prBinBSWiMS$ROC.analysis$roc.predictor and
prBinRIDGE$ROC.analysis$roc.predictor
| 9.44 |
3.86e-21 * * * |
two.sided |
0.874 |
0.591 |
Feature Analysis
fs <- bConvml$bagging$frequencyTable
barplot(fs[order(-fs)],las=2,main="Selected Features",cex.names = 0.5)

sm <- summary(bConvml)
summary(TADPOLE_Conv_TRAINNorm$M_ST39CV)
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> -2.7659 -0.5863 0.2002 0.0000 0.6914 2.4492
pander::pander(bConvml$formula.list)
Surv(TimeToEvent, status) ~ 1 + FAQ + RAVLT_immediate + ADAS13 +
ABETA + PTAU + M_ST13TA + M_ST56SA + RD_ST34CV + RD_ST49SA,
Surv(TimeToEvent, status) ~ 1 + ADAS11 + TAU + RD_ST34SA + M_ST29SV
+ M_ST56CV + APOE4, =-=End=-=, Surv(TimeToEvent,
status) ~ 1 + ADAS13 + FAQ + RAVLT_immediate + ABETA + PTAU + M_ST56SA +
M_ST13TA + RD_ST49SA + RD_ST34CV, =-=End=-=,
Surv(TimeToEvent, status) ~ 1 + RAVLT_immediate + FAQ + ADAS13 +
ABETA + PTAU + M_ST56CV, Surv(TimeToEvent, status) ~ 1 + ADAS11
+ TAU + M_ST29SV + RD_ST34SA + M_ST14TS + M_ST11SV + M_ST56SA +
APOE4, =-=End=-=, Surv(TimeToEvent, status) ~ 1 + FAQ
+ RAVLT_immediate + ABETA + PTAU + M_ST56SA + M_ST13TA + RD_ST34CV,
=-=End=-=, Surv(TimeToEvent, status) ~ 1 + ADAS13 + FAQ +
RAVLT_immediate + ABETA + PTAU + M_ST59CV + M_ST11SV + M_ST56SA +
RD_ST49SA, Surv(TimeToEvent, status) ~ 1 + ADAS11 + TAU +
M_ST29SV + M_ST56CV + APOE4, =-=End=-=,
Surv(TimeToEvent, status) ~ 1 + RAVLT_immediate + ADAS13 + FAQ +
ABETA + M_ST56SA + M_ST13TA + PTAU, Surv(TimeToEvent, status) ~
1 + ADAS11 + TAU + M_ST11SV + M_ST56CV + M_ST24CV + M_ST59SA + RD_ST49SA
+ APOE4 + RD_ST34SA, =-=End=-=, Surv(TimeToEvent,
status) ~ 1 + FAQ + ADAS13 + RAVLT_immediate + ABETA + TAU + M_ST39CV +
M_ST56SA + RD_ST34CV + M_ST13CV, Surv(TimeToEvent, status) ~ 1
+ ADAS11 + PTAU + RAVLT_perc_forgetting + M_ST29SV + M_ST11SV + M_ST14TS
+ M_ST59SA + RD_ST49SA, =-=End=-=, Surv(TimeToEvent,
status) ~ 1 + ADAS13 + FAQ + RAVLT_immediate + M_ST56SA + ABETA + TAU +
M_ST13CV + M_ST39SA, Surv(TimeToEvent, status) ~ 1 + ADAS11 +
APOE4 + M_ST56CV + PTAU + M_ST12SV, Surv(TimeToEvent, status) ~
1 + RAVLT_perc_forgetting + M_ST29SV + M_ST13TA + MMSE + RD_ST34SA +
M_ST14TS + M_ST59SA, =-=End=-=, Surv(TimeToEvent,
status) ~ 1 + RAVLT_immediate + FAQ + ADAS13 + ABETA + M_ST56CV +
PTAU, Surv(TimeToEvent, status) ~ 1 + ADAS11 + TAU + M_ST29SV +
M_ST11SV + M_ST14TS + M_ST56SA + RD_ST34SA, Surv(TimeToEvent,
status) ~ 1 + RAVLT_perc_forgetting + MMSE + M_ST12SV + APOE4 +
M_ST13TA, =-=End=-=, Surv(TimeToEvent, status) ~ 1 +
FAQ + RAVLT_immediate + ABETA + M_ST56SA + M_ST13TA + RD_ST15TS + TAU +
RD_ST34CV, =-=End=-=, Surv(TimeToEvent, status) ~ 1 +
FAQ + RAVLT_immediate + ADAS13 + ABETA + PTAU + M_ST56SA + M_ST13TA +
RD_ST34CV + RD_ST49SA, Surv(TimeToEvent, status) ~ 1 + ADAS11 +
TAU + RAVLT_perc_forgetting + M_ST56CV + APOE4 + M_ST29SV +
M_ST14TS, =-=End=-=, Surv(TimeToEvent, status) ~ 1 +
ADAS13 + FAQ + RAVLT_immediate + M_ST56SA + ABETA + M_ST13TA + PTAU +
RD_ST34CV + RD_ST49SA, =-=End=-=, Surv(TimeToEvent,
status) ~ 1 + FAQ + ADAS13 + RAVLT_immediate + M_ST56SA + PTAU + ABETA +
M_ST13TA + RD_ST49SA + RD_ST34CV, Surv(TimeToEvent, status) ~ 1
+ ADAS11 + TAU + M_ST56CV + M_ST14TS + M_ST29SV + APOE4,
=-=End=-=, Surv(TimeToEvent, status) ~ 1 + FAQ + ADAS13 +
RAVLT_immediate + ABETA + M_ST56SA + M_ST13TA + PTAU + RD_ST34CV +
RD_ST49SA, Surv(TimeToEvent, status) ~ 1 + ADAS11 + TAU +
RD_ST34SA + M_ST56CV + APOE4 + RAVLT_perc_forgetting + M_ST29SV +
M_ST14TS, =-=End=-=, Surv(TimeToEvent, status) ~ 1 +
FAQ + ADAS13 + RAVLT_immediate + ABETA + M_ST56SA + PTAU + M_ST13TA +
RD_ST34CV + RD_ST49SA, =-=End=-=, Surv(TimeToEvent,
status) ~ 1 + FAQ + RAVLT_immediate + ABETA + TAU + M_ST11SV + M_ST59SA
+ RD_ST15TS + M_ST24CV, Surv(TimeToEvent, status) ~ 1 + ADAS13
+ PTAU + M_ST56SA + M_ST29SV + M_ST26CV, =-=End=-=,
Surv(TimeToEvent, status) ~ 1 + ADAS13 + RAVLT_immediate + FAQ +
M_ST56SA + M_ST13TA + ABETA + PTAU + RD_ST34CV + RD_ST49SA,
Surv(TimeToEvent, status) ~ 1 + ADAS11 + TAU + RD_ST34SA + M_ST11SV
+ M_ST29SV + APOE4 + M_ST59SA, =-=End=-=,
Surv(TimeToEvent, status) ~ 1 + FAQ + ADAS13 + RAVLT_immediate +
ABETA + PTAU + M_ST56CV + M_ST13CV, Surv(TimeToEvent, status) ~
1 + ADAS11 + TAU + M_ST29SV + M_ST11SV + M_ST56SA + APOE4 +
M_ST14TS, =-=End=-=, Surv(TimeToEvent, status) ~ 1 +
RAVLT_immediate + FAQ + ADAS13 + ABETA + TAU + M_ST56SA + M_ST13TA +
RD_ST34CV + RD_ST49SA, =-=End=-=, Surv(TimeToEvent,
status) ~ 1 + FAQ + ADAS13 + RAVLT_immediate + M_ST56SA + ABETA + PTAU +
M_ST13TA + RD_ST34CV + RD_ST49SA, Surv(TimeToEvent, status) ~ 1
+ ADAS11 + TAU + M_ST56CV + M_ST11SV + APOE4 + M_ST24CV + M_ST59SA
and =-=End=-=
pander::pander(bConvml$bagging$predfit$coef)
| 0.061 |
5.89e-17 |
0.35 |
0.136 |
-0.262 |
0.0422 |
0.159 |
0.0733 |
0.27 |
-0.021 |
0.392 |
cnames <- names(bConvml$bagging$bagged.model$coefficients)
pander::pander(cbind(
bConvml$bagging$bagged.model$coefficients,
bConvml$bagging$bagged.model$baggingAnalysis$coefficients[cnames],
bConvml$bagging$bagged.model$baggingAnalysis$wts[cnames],
bConvml$bagging$bagged.model$baggingAnalysis$avgLogPvalues[cnames],
bConvml$bagging$bagged.model$baggingAnalysis$RelativeFrequency[cnames])
)
| (Intercept) |
0.00e+00 |
NA |
NA |
NA |
NA |
| FAQ |
2.46e-01 |
0.4578 |
3.98e-02 |
4.77 |
1.00 |
| RAVLT_immediate |
-3.44e-01 |
-0.6401 |
3.98e-02 |
5.57 |
1.00 |
| ABETA |
-2.08e-01 |
-0.3869 |
3.98e-02 |
3.35 |
1.00 |
| M_ST56SA |
-2.16e-01 |
-0.3667 |
4.38e-02 |
5.06 |
1.00 |
| ADAS13 |
1.24e-01 |
0.4061 |
2.52e-02 |
2.60 |
0.90 |
| PTAU |
1.38e-02 |
0.3358 |
3.39e-03 |
3.80 |
0.90 |
| TAU |
3.14e-01 |
0.3815 |
7.64e-02 |
4.80 |
0.80 |
| M_ST13TA |
-2.04e-01 |
-0.4165 |
4.85e-02 |
8.36 |
0.75 |
| ADAS11 |
1.91e-01 |
0.5819 |
3.74e-02 |
8.11 |
0.65 |
| RD_ST34CV |
-8.86e-02 |
-0.2497 |
4.05e-02 |
4.03 |
0.65 |
| RD_ST49SA |
-8.66e-02 |
-0.2180 |
4.54e-02 |
2.94 |
0.65 |
| M_ST29SV |
-1.17e-01 |
-0.4415 |
3.27e-02 |
3.56 |
0.60 |
| APOE4 |
3.15e-01 |
0.7243 |
5.38e-02 |
3.46 |
0.60 |
| M_ST56CV |
-2.26e-02 |
-0.2461 |
1.24e-02 |
4.59 |
0.55 |
| M_ST11SV |
-1.56e-01 |
-0.3062 |
8.40e-02 |
3.89 |
0.45 |
| M_ST14TS |
5.94e-02 |
0.2248 |
4.90e-02 |
3.26 |
0.40 |
| RD_ST34SA |
-1.02e-01 |
-0.2870 |
7.55e-02 |
2.74 |
0.35 |
| M_ST59SA |
-8.52e-02 |
-0.2818 |
7.48e-02 |
3.67 |
0.30 |
| RAVLT_perc_forgetting |
7.07e-02 |
0.5214 |
4.03e-02 |
3.16 |
0.25 |
| M_ST24CV |
-1.02e-01 |
-0.3723 |
1.36e-01 |
3.54 |
0.15 |
| M_ST13CV |
-4.86e-13 |
-0.2404 |
1.00e-12 |
3.33 |
0.15 |
| MMSE |
-3.99e-02 |
-0.2940 |
1.01e-01 |
2.69 |
0.10 |
| M_ST12SV |
-3.66e-02 |
-0.3418 |
7.96e-02 |
3.35 |
0.10 |
| RD_ST15TS |
-5.97e-02 |
-0.2581 |
1.72e-01 |
3.23 |
0.10 |
| M_ST26CV |
-1.95e-13 |
-0.2891 |
1.00e-12 |
2.86 |
0.05 |
| M_ST39CV |
-9.17e-14 |
-0.1361 |
1.00e-12 |
4.20 |
0.05 |
| M_ST59CV |
-1.68e-13 |
-0.2491 |
1.00e-12 |
4.81 |
0.05 |
| M_ST39SA |
-4.15e-14 |
-0.0615 |
1.00e-12 |
3.02 |
0.05 |
pander::pander(sm$coefficients)
| ADAS11 |
1.91e-01 |
1.463 |
1.789 |
2.189 |
0.668 |
0.722 |
0.752 |
0.679 |
0.757 |
0.782 |
0.06175 |
0.539 |
5.96 |
5.24 |
0.025417 |
0.65 |
| M_ST13TA |
-2.04e-01 |
0.572 |
0.659 |
0.760 |
0.657 |
0.742 |
0.766 |
0.668 |
0.766 |
0.794 |
0.04056 |
0.663 |
5.44 |
6.72 |
0.027437 |
0.75 |
| RAVLT_immediate |
-3.44e-01 |
0.400 |
0.527 |
0.695 |
0.673 |
0.755 |
0.769 |
0.718 |
0.787 |
0.800 |
0.04894 |
0.628 |
5.36 |
6.54 |
0.013008 |
1.00 |
| TAU |
3.14e-01 |
1.224 |
1.465 |
1.753 |
0.655 |
0.748 |
0.762 |
0.638 |
0.782 |
0.793 |
0.03016 |
0.544 |
4.37 |
5.31 |
0.010720 |
0.80 |
| M_ST56SA |
-2.16e-01 |
0.586 |
0.693 |
0.819 |
0.566 |
0.759 |
0.768 |
0.577 |
0.789 |
0.797 |
0.02960 |
0.468 |
4.31 |
4.59 |
0.008198 |
1.00 |
| FAQ |
2.46e-01 |
1.273 |
1.581 |
1.963 |
0.708 |
0.732 |
0.769 |
0.688 |
0.767 |
0.800 |
0.03459 |
0.371 |
4.22 |
3.55 |
0.032788 |
1.00 |
| M_ST59CV |
-1.68e-13 |
0.693 |
0.780 |
0.876 |
0.614 |
0.751 |
0.766 |
0.628 |
0.779 |
0.792 |
0.01627 |
0.307 |
4.16 |
2.92 |
0.013338 |
0.05 |
| M_ST59SA |
-8.52e-02 |
0.645 |
0.754 |
0.883 |
0.546 |
0.749 |
0.749 |
0.554 |
0.783 |
0.782 |
0.02014 |
0.445 |
3.96 |
4.32 |
-0.000775 |
0.30 |
| RD_ST34CV |
-8.86e-02 |
0.683 |
0.779 |
0.888 |
0.520 |
0.759 |
0.777 |
0.542 |
0.786 |
0.806 |
0.01663 |
0.443 |
3.90 |
4.40 |
0.020088 |
0.65 |
| RAVLT_perc_forgetting |
7.07e-02 |
1.224 |
1.684 |
2.319 |
0.652 |
0.728 |
0.738 |
0.673 |
0.750 |
0.762 |
0.03863 |
0.520 |
3.85 |
5.13 |
0.012586 |
0.25 |
| M_ST39CV |
-9.17e-14 |
0.814 |
0.873 |
0.936 |
0.650 |
0.756 |
0.764 |
0.642 |
0.783 |
0.794 |
0.00924 |
0.346 |
3.83 |
3.30 |
0.011278 |
0.05 |
| ABETA |
-2.08e-01 |
0.541 |
0.679 |
0.853 |
0.609 |
0.782 |
0.769 |
0.672 |
0.808 |
0.800 |
0.02112 |
0.430 |
3.76 |
4.56 |
-0.007637 |
1.00 |
| M_ST29SV |
-1.17e-01 |
0.500 |
0.643 |
0.826 |
0.673 |
0.751 |
0.752 |
0.692 |
0.777 |
0.782 |
0.02558 |
0.498 |
3.69 |
4.89 |
0.005547 |
0.60 |
| M_ST11SV |
-1.56e-01 |
0.625 |
0.736 |
0.868 |
0.622 |
0.743 |
0.752 |
0.635 |
0.771 |
0.784 |
0.01769 |
0.375 |
3.66 |
3.60 |
0.013446 |
0.45 |
| M_ST12SV |
-3.66e-02 |
0.581 |
0.711 |
0.869 |
0.673 |
0.721 |
0.739 |
0.679 |
0.739 |
0.762 |
0.02226 |
0.421 |
3.58 |
4.05 |
0.022628 |
0.10 |
| M_ST24CV |
-1.02e-01 |
0.557 |
0.689 |
0.852 |
0.645 |
0.737 |
0.750 |
0.647 |
0.774 |
0.784 |
0.02191 |
0.436 |
3.50 |
4.20 |
0.010169 |
0.15 |
| PTAU |
1.38e-02 |
1.165 |
1.399 |
1.680 |
0.662 |
0.759 |
0.772 |
0.644 |
0.790 |
0.798 |
0.02007 |
0.392 |
3.44 |
3.75 |
0.007735 |
0.90 |
| APOE4 |
3.15e-01 |
1.357 |
2.063 |
3.136 |
0.594 |
0.739 |
0.749 |
0.603 |
0.765 |
0.777 |
0.02337 |
0.409 |
3.41 |
3.94 |
0.011835 |
0.60 |
| RD_ST15TS |
-5.97e-02 |
0.661 |
0.773 |
0.903 |
0.520 |
0.746 |
0.753 |
0.555 |
0.781 |
0.790 |
0.01487 |
0.390 |
3.36 |
3.96 |
0.008388 |
0.10 |
| M_ST13CV |
-4.86e-13 |
0.682 |
0.786 |
0.907 |
0.629 |
0.765 |
0.758 |
0.647 |
0.793 |
0.787 |
0.01359 |
0.364 |
3.28 |
3.52 |
-0.006338 |
0.15 |
| M_ST39SA |
-4.15e-14 |
0.904 |
0.940 |
0.978 |
0.655 |
0.746 |
0.751 |
0.655 |
0.775 |
0.783 |
0.00326 |
0.254 |
3.10 |
2.41 |
0.007519 |
0.05 |
| M_ST14TS |
5.94e-02 |
1.094 |
1.252 |
1.433 |
0.594 |
0.747 |
0.752 |
0.598 |
0.775 |
0.782 |
0.01306 |
0.257 |
3.07 |
2.44 |
0.007519 |
0.40 |
| M_ST26CV |
-1.95e-13 |
0.620 |
0.749 |
0.905 |
0.637 |
0.749 |
0.731 |
0.643 |
0.772 |
0.755 |
0.01495 |
0.406 |
2.99 |
3.89 |
-0.017097 |
0.05 |
| RD_ST49SA |
-8.66e-02 |
0.699 |
0.804 |
0.925 |
0.503 |
0.764 |
0.773 |
0.538 |
0.792 |
0.800 |
0.01102 |
0.258 |
2.95 |
2.53 |
0.007946 |
0.65 |
| RD_ST34SA |
-1.02e-01 |
0.619 |
0.750 |
0.911 |
0.515 |
0.740 |
0.751 |
0.544 |
0.764 |
0.780 |
0.01448 |
0.172 |
2.80 |
1.66 |
0.016271 |
0.35 |
| M_ST56CV |
-2.26e-02 |
0.694 |
0.782 |
0.881 |
0.645 |
0.741 |
0.749 |
0.653 |
0.768 |
0.775 |
0.01087 |
0.262 |
2.79 |
2.48 |
0.007591 |
0.55 |
| MMSE |
-3.99e-02 |
0.610 |
0.745 |
0.911 |
0.685 |
0.721 |
0.738 |
0.672 |
0.743 |
0.762 |
0.01543 |
0.384 |
2.76 |
3.67 |
0.019400 |
0.10 |
| ADAS13 |
1.24e-01 |
1.130 |
1.501 |
1.993 |
0.713 |
0.781 |
0.780 |
0.721 |
0.809 |
0.808 |
0.01274 |
0.203 |
2.44 |
1.92 |
-0.000754 |
0.90 |
pander::pander(bConvml$univariate[bConvml$selectedfeatures,])
| FAQ |
FAQ |
FAQ |
7.57 |
| RAVLT_immediate |
RAVLT_immediate |
RAVLT_immediate |
10.41 |
| ABETA |
ABETA |
ABETA |
8.51 |
| M_ST56SA |
M_ST56SA |
M_ST56SA |
4.71 |
| ADAS13 |
ADAS13 |
ADAS13 |
10.85 |
| PTAU |
PTAU |
PTAU |
5.59 |
| TAU |
TAU |
TAU |
5.29 |
| M_ST13TA |
M_ST13TA |
M_ST13TA |
7.42 |
| ADAS11 |
ADAS11 |
ADAS11 |
9.39 |
| RD_ST34CV |
RD_ST34CV |
RD_ST34CV |
2.53 |
| RD_ST49SA |
RD_ST49SA |
RD_ST49SA |
1.82 |
| M_ST29SV |
M_ST29SV |
M_ST29SV |
8.57 |
| APOE4 |
APOE4 |
APOE4 |
3.97 |
| M_ST56CV |
M_ST56CV |
M_ST56CV |
7.17 |
| M_ST11SV |
M_ST11SV |
M_ST11SV |
5.89 |
| M_ST14TS |
M_ST14TS |
M_ST14TS |
5.15 |
| RD_ST34SA |
RD_ST34SA |
RD_ST34SA |
2.91 |
| M_ST59SA |
M_ST59SA |
M_ST59SA |
3.24 |
| RAVLT_perc_forgetting |
RAVLT_perc_forgetting |
RAVLT_perc_forgetting |
7.08 |
| M_ST24CV |
M_ST24CV |
M_ST24CV |
7.09 |
| M_ST13CV |
M_ST13CV |
M_ST13CV |
6.71 |
| MMSE |
MMSE |
MMSE |
7.13 |
| M_ST12SV |
M_ST12SV |
M_ST12SV |
8.36 |
| RD_ST15TS |
RD_ST15TS |
RD_ST15TS |
2.14 |
| M_ST26CV |
M_ST26CV |
M_ST26CV |
7.12 |
| M_ST39CV |
M_ST39CV |
M_ST39CV |
6.44 |
| M_ST59CV |
M_ST59CV |
M_ST59CV |
6.33 |
| M_ST39SA |
M_ST39SA |
M_ST39SA |
6.67 |
#ptestl <- predict(bConvml,TADPOLE_Conv_TEST,type="lp")
ptestl <- predict(bConvml,TADPOLE_Conv_TESTNorm,type="lp")
boxplot(ptestl~TADPOLE_Conv_TEST$status)

#ptestr <- predict(bConvml,TADPOLE_Conv_TEST,type="risk")
ptestr <- predict(bConvml,TADPOLE_Conv_TESTNorm,type="risk")
eventCases <- subset(TADPOLE_Conv_TEST,status==1)
plot(1.0/ptestr[rownames(eventCases)]~eventCases$TimeToEvent)

pander::pander(cor.test(eventCases$TimeToEvent,1.0/ptestr[rownames(eventCases)],method="spearman"))
Spearman’s rank correlation rho:
eventCases$TimeToEvent and
1/ptestr[rownames(eventCases)]
| 18210 |
0.000551 * * * |
two.sided |
0.44 |
perdsurv <- as.data.frame(cbind(Times=TADPOLE_Conv_TEST$TimeToEvent,
Outcome=TADPOLE_Conv_TEST$status,
LinearPredictors=ptestl,
ptestr))
boxplot(perdsurv$LinearPredictors~perdsurv$Outcome)

prSurv <- predictionStats_survival(perdsurv,"BSWiMS: MCI to AD Conversion")


pander::pander(prSurv$CIRisk)
pander::pander(prSurv$CILp)
pander::pander(prSurv$spearmanCI)
prBin <- predictionStats_binary(cbind(TADPOLE_Conv_TEST$status,ptestl),"BSWiMS: MCI to AD Conversion")

pander::pander(prBin$aucs)
pander::pander(prBin$CM.analysis$tab)
| Test + |
56 |
34 |
90 |
| Test - |
2 |
78 |
80 |
| Total |
58 |
112 |
170 |
par(op)
ho <- mean(TADPOLE_Conv_TRAIN$status)
timeInterval <- mean(TADPOLE_Conv_TRAIN[TADPOLE_Conv_TRAIN$status==0,"TimeToEvent"])
pgzero <- ppoisGzero(perdsurv$LinearPredictors,ho)
rsdata <- cbind(perdsurv$Outcome,pgzero,perdsurv$Times)
riskAnalysis <- RRPlot(rsdata,riskTimeInterval=timeInterval,title="Test")
#> [1] 0.3411765
#> [1] 0.3411765 1.0000000




#> [1] 0.8996088 0.9408211 0.4599589 3.5649262 6.6280369 14.8752056 1.0000000
#> [8] 0.9534954


pander::pander(riskAnalysis$keyPoints)
| @:0.9 |
0.480 |
4.71 |
2.963 |
7.50e+00 |
0.724 |
0.889 |
0.807 |
0.155 |
| @:0.8 |
0.311 |
10.66 |
4.525 |
2.51e+01 |
0.914 |
0.781 |
0.847 |
0.235 |
| @MAX_BACC |
0.285 |
46.28 |
6.586 |
3.25e+02 |
0.983 |
0.738 |
0.860 |
0.256 |
| @MAX_RR |
0.186 |
300.69 |
0.614 |
1.47e+05 |
1.000 |
0.571 |
0.786 |
0.271 |
| @SEN100 |
0.186 |
300.69 |
0.614 |
1.47e+05 |
1.000 |
0.571 |
0.786 |
0.271 |
| p(0.5) |
0.500 |
4.84 |
3.045 |
7.69e+00 |
0.724 |
0.899 |
0.812 |
0.153 |
pander::pander(riskAnalysis$c.index)
C Index: 0.874
Dxy: 0.747
S.D.: 0.0383
n: 170
missing: 0
uncensored: 58
Relevant Pairs: 13252
Concordant: 11576
Uncertain: 15470
cstatCI:
pander::pander(riskAnalysis$ROCAnalysis$aucs)
pander::pander(riskAnalysis$cenAUC)
0.928
pander::pander(riskAnalysis$ROCAnalysis$ClassMetrics)
accci:
senci:
speci:
aucci:
berci:
preci:
F1ci:
pander::pander(riskAnalysis$surdif)
Call: survival::Surv(eTime, eStatus) ~ class Chisq = 83.430643
on 2 degrees of freedom, p = 0.000000
| class=0 |
88 |
5 |
35.87 |
26.57 |
71.78 |
| class=1 |
23 |
11 |
7.65 |
1.46 |
1.69 |
| class=2 |
59 |
42 |
14.47 |
52.37 |
72.24 |